Neural Analyses
Dani Cosme
2021-03-25
define color palettes and labels
pal_self_other = c("#FFA90A", "#247BA0")
pal_social_academic = c("#63647E", "#F25F5C")
pal_wave = c("#693668", "#A74482", "#F84AA7")
pal_label = c("#47A8BD", "#DBC057", "#FF3366")
pal_gender = c("#70c1b3","#247BA0")
parcel_labeller = labeller(label = c('social' = 'social parcels', 'other' = 'control parcels', 'self' = 'self parcels'),
domain = c('social' = 'social domain', 'academic' = 'academic domain'),
wave = c("t1" = "wave 1", "t2" = "wave 2", "t3" = "wave 3"))
label_df = expand.grid(label = c("social", "self", "other"),
target = c("self", "other"),
domain = c("social", "academic"),
age = 13,
expected_avg = 1,
expected_diff = 1)
dcbw = #readRDS("~/dc_bw.Rds") +
theme_classic() +
theme(text = element_text(size = 14, family = "Futura Medium", color = "black"),
panel.background = element_blank(),
plot.background = element_blank(),
strip.background = element_blank(),
strip.text = element_text(size = 14),
legend.background = element_rect(fill = NA, color = NA),
axis.line = element_line(color = "black"),
axis.text = element_text(color = "black"),
panel.grid.minor = element_blank())load MRI data
- exclude participants with >20% volumes with motion artifacts or low quality FX data
- standardize betas within parcel (across participants and time)
- recode standardized betas +/- 3 SDs from the mean as NA (0.8% of all observations)
# mri
# self_parcels = c(5, 17, 28, 47, 52, 54, 63, 66, 91, 116, 131, 139, 144, 147, 152, 156, 184, 198, 207, 225, 246, 249, 282, 292, 300, 301, 305, 309, 353, 354, 380, 399)
# social_parcels = c(4, 18, 20, 23, 29, 34, 49, 54, 59, 60, 62, 63, 66, 67, 76, 82, 111, 114, 116, 117, 139, 143, 146, 150, 152, 178, 179, 184, 189, 191, 203, 212, 224, 229, 236, 237, 238, 239, 241, 245, 246, 250, 259, 260, 266, 271, 273, 292, 301, 305, 309, 310, 322, 324, 328, 331, 333, 342, 343, 350, 353, 354, 369, 374, 391)
self_parcels = c(5, 17, 28, 47, 52, 66, 116, 147, 152, 156, 184, 198, 207, 225, 249, 292, 309, 354, 380)
social_parcels = c(18, 23, 29, 49, 54, 59, 62, 63, 67, 76, 111, 114, 139, 143, 146, 150, 178, 179, 189, 203, 212, 224, 229, 236, 238, 239, 245, 250, 259, 266, 271, 301, 305, 310, 322, 324, 328, 331, 333, 342, 343, 350, 374, 391)
mri_exclusions = c('s002_t1', 's004_t1', 's008_t1', 's011_t1', 's017_t1',
's026_t1', 's033_t2', 's034_t1', 's041_t1', 's044_t1',
's047_t1', 's051_t1', 's054_t1', 's057_t1', 's059_t1',
's061_t1', 's063_t1', 's070_t2', 's074_t1', 's074_t2',
's078_t1', 's084_t1', 's090_t2', 's090_t3', 's094_t1',
's094_t2', 's096_t1')
parcellations = read_csv('../data/fxParcellations.csv') %>%
mutate(label = ifelse(parcellation %in% self_parcels, 'self',
ifelse(parcellation %in% social_parcels, 'social', 'other'))) %>%
mutate(wave = paste0("t", as.numeric(c(`10` = 1, `13` = 2, `16` = 3)[as.character(age)]))) %>%
select(-age) %>%
unite(sub_wave, c(subjectID, wave), remove = FALSE) %>%
group_by(parcellation) %>%
mutate(inclusion = ifelse(sub_wave %in% mri_exclusions, "excluded from MRI", "completed MRI"),
beta = ifelse(sub_wave %in% mri_exclusions, NA, beta),
sd = ifelse(sub_wave %in% mri_exclusions, NA, sd),
beta_std = scale(beta, center = FALSE, scale = TRUE),
mean_beta_std = mean(beta_std, na.rm = TRUE)) %>%
select(-sub_wave) %>%
ungroup()
# parcellations %>%
# ggplot(aes(beta_std, fill = label)) +
# geom_density(color = NA, alpha = .5) +
# facet_grid(~wave) +
# dcbw
#
# psych::describe.by(parcellations$beta_std, group = parcellations$label)
#
# parcellations %>%
# filter(beta_std > mean_beta_std + 3 | beta_std < mean_beta_std - 3) %>%
# group_by(subjectID, wave) %>%
# summarize(n = n()) %>%
# arrange(desc(n))
#
# parcellations %>%
# filter(beta_std > mean_beta_std + 3 | beta_std < mean_beta_std - 3) %>%
# group_by(label) %>%
# summarize(n = n()) %>%
# ungroup() %>%
# mutate(percent = round((sum(n) / nrow(filter(parcellations, !is.na(beta)))) * 100, 2))
#
# parcellations %>%
# filter(beta_std > mean_beta_std + 3 | beta_std < mean_beta_std - 3) %>%
# group_by(label) %>%
# summarize(meanOutlier = mean(beta_std, na.rm = TRUE),
# sdOutlier = sd(beta_std, na.rm = TRUE))
parcellations_ex = parcellations %>%
mutate(beta_std = ifelse(beta_std > mean_beta_std + 3 | beta_std < mean_beta_std - 3, NA, beta_std))load demographic data and merge
# demographics
demo = read.csv("../data/SFIC_age.pds.gender.csv") %>%
rename("subjectID" = SID,
"wave" = wavenum,
"gender" = Gender) %>%
mutate(subjectID = sprintf("s%03d", subjectID),
wave = paste0("t", wave),
age_c = age - 13,
age_c2 = age_c^2,
pdss_c = pdss - 3,
pdss_c2 = pdss_c^2)
# merge data
merged = parcellations_ex %>%
full_join(., demo, by = c("subjectID", "wave")) %>%
mutate(inclusion = ifelse(is.na(inclusion), "didn't complete MRI", inclusion)) %>%
filter(!(subjectID == "s086" & wave == "t3")) #no MRI, task, or self-report data was collected
# subset data for modeling
neuro_model_data = merged %>%
filter(!is.na(beta)) %>%
select(subjectID, wave, age, age_c, age_c2, target, domain, parcellation, label, beta, beta_std)
neuro_model_data_ex = neuro_model_data %>%
na.omit()
# dummy code target and domain
neuro_model_data_dummy = neuro_model_data_ex %>%
mutate(target = ifelse(target == "self", .5, -.5),
domain = ifelse(domain == "social", .5, -.5))sample descriptives
full sample
merged %>%
select(subjectID, wave, age, gender) %>%
unique() %>%
group_by(wave) %>%
summarize(n = n(),
meanAge = mean(age, na.rm = TRUE),
sdAge = sd(age, na.rm = TRUE)) %>%
kable(format = 'pandoc', digits = 2)| wave | n | meanAge | sdAge |
|---|---|---|---|
| t1 | 90 | 10.07 | 0.31 |
| t2 | 57 | 13.04 | 0.31 |
| t3 | 44 | 16.46 | 0.58 |
merged %>%
select(subjectID, wave, age, gender) %>%
unique() %>%
group_by(wave, gender) %>%
summarize(n = n()) %>%
spread(gender, n) %>%
kable(format = 'pandoc', digits = 2)| wave | F | M |
|---|---|---|
| t1 | 45 | 45 |
| t2 | 30 | 27 |
| t3 | 25 | 19 |
broken down by inclusion
age_table = merged %>%
select(subjectID, inclusion, wave, age, pdss, gender) %>%
unique() %>%
group_by(inclusion, wave) %>%
summarize(N = n(),
Mage = mean(age, na.rm = TRUE),
SDage = sd(age, na.rm = TRUE),
Mpdss = mean(pdss, na.rm = TRUE),
SDpdss = sd(pdss, na.rm = TRUE))
gender_table = merged %>%
select(subjectID, inclusion, wave, age, pds, gender) %>%
unique() %>%
group_by(inclusion, wave, gender) %>%
summarize(N = n()) %>%
spread(gender, N) %>%
rename("Female" = F,
"Male" = M)
age_table %>%
left_join(gender_table) %>%
extract(wave, "Wave", "t([1-3]{1})") %>%
arrange(Wave) %>%
select(Wave, inclusion, N, Mage, SDage, Mpdss, SDpdss, Female, Male) %>%
rename("MRI status" = inclusion) %>%
kable(format = 'pandoc', digits = 2)| Wave | MRI status | N | Mage | SDage | Mpdss | SDpdss | Female | Male |
|---|---|---|---|---|---|---|---|---|
| 1 | completed MRI | 57 | 10.08 | 0.32 | 2.16 | 0.74 | 33 | 24 |
| 1 | didn’t complete MRI | 12 | 10.00 | 0.25 | 2.00 | 0.77 | 4 | 8 |
| 1 | excluded from MRI | 21 | 10.07 | 0.33 | 1.83 | 0.58 | 8 | 13 |
| 2 | completed MRI | 44 | 13.06 | 0.33 | 3.57 | 1.05 | 25 | 19 |
| 2 | didn’t complete MRI | 8 | 13.07 | 0.20 | 3.69 | 0.65 | 4 | 4 |
| 2 | excluded from MRI | 5 | 12.79 | 0.28 | 2.62 | 0.85 | 1 | 4 |
| 3 | completed MRI | 34 | 16.33 | 0.46 | 4.75 | 0.39 | 19 | 15 |
| 3 | didn’t complete MRI | 9 | 17.06 | 0.60 | 4.78 | 0.67 | 6 | 3 |
| 3 | excluded from MRI | 1 | 15.72 | NA | 3.50 | NA | NA | 1 |
plot
full sample
merged %>%
select(subjectID, wave, gender, age, inclusion) %>%
group_by(subjectID) %>%
unique() %>%
mutate(n.waves = n()) %>%
ungroup() %>%
arrange(n.waves, gender, age, inclusion) %>%
mutate(order = row_number()) %>%
ggplot(aes(age, reorder(subjectID, -order), color = gender)) +
geom_line(size = .3) +
geom_point(aes(shape = inclusion), size = 2, fill = "white") +
scale_color_manual(values = pal_gender, name = "", labels = c("female", "male")) +
scale_shape_manual(name = "", values = c(19, 17, 21)) +
labs(x = "\nage", y = "participant\n") +
dcbw +
theme(axis.line = element_line(colour = "black"),
axis.text.y = element_blank(),
axis.ticks.y = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
legend.position = c(.75,.92),
legend.spacing.y = unit(.01, 'cm'),
legend.margin = unit(0, "cm"))
MRI only
merged %>%
filter(!inclusion == "didn't complete MRI") %>%
mutate(inclusion = ifelse(grepl("excluded", inclusion), "excluded", "included")) %>%
select(subjectID, wave, gender, age, inclusion) %>%
group_by(subjectID) %>%
unique() %>%
mutate(n.waves = n()) %>%
ungroup() %>%
arrange(n.waves, gender, age, inclusion) %>%
mutate(order = row_number()) %>%
ggplot(aes(age, reorder(subjectID, -order), color = gender)) +
geom_line(size = .3) +
geom_point(aes(shape = inclusion), size = 2, fill = "white") +
scale_color_manual(values = pal_gender, name = "", labels = c("female", "male")) +
scale_shape_manual(name = "", values = c(21, 19)) +
labs(x = "\nage", y = "participant\n") +
dcbw +
theme(axis.line = element_line(colour = "black"),
axis.text.y = element_blank(),
axis.ticks.y = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
legend.position = c(.75,.92),
legend.spacing.y = unit(.01, 'cm'),
legend.margin = unit(0, "cm"))
descriptives
# collapsed across wave
neuro_model_data_dummy %>%
mutate(target = ifelse(target == .5, "self", "other"),
domain = ifelse(domain == .5, "social", "academic")) %>%
group_by(domain, label) %>%
summarize(M = mean(beta_std, na.rm = TRUE),
SD = sd(beta_std, na.rm = TRUE)) %>%
gather(var, value, M, SD) %>%
unite(label, label, var, sep = " ") %>%
spread(label, value) %>%
kable(format = "pandoc", digits = 2)| domain | other M | other SD | self M | self SD | social M | social SD |
|---|---|---|---|---|---|---|
| academic | 0.01 | 0.92 | -0.08 | 0.91 | 0.14 | 0.92 |
| social | -0.01 | 0.95 | 0.02 | 0.92 | 0.27 | 0.93 |
neuro_model_data_dummy %>%
mutate(target = ifelse(target == .5, "self", "other"),
domain = ifelse(domain == .5, "social", "academic")) %>%
group_by(target, label) %>%
summarize(M = mean(beta_std, na.rm = TRUE),
SD = sd(beta_std, na.rm = TRUE)) %>%
gather(var, value, M, SD) %>%
unite(label, label, var, sep = " ") %>%
spread(label, value) %>%
kable(format = "pandoc", digits = 2)| target | other M | other SD | self M | self SD | social M | social SD |
|---|---|---|---|---|---|---|
| other | 0.00 | 0.94 | -0.11 | 0.91 | 0.22 | 0.93 |
| self | -0.01 | 0.94 | 0.05 | 0.92 | 0.19 | 0.93 |
# as a function of wave
neuro_model_data_dummy %>%
mutate(target = ifelse(target == .5, "self", "other"),
domain = ifelse(domain == .5, "social", "academic")) %>%
group_by(domain, label, wave) %>%
summarize(M = mean(beta_std, na.rm = TRUE),
SD = sd(beta_std, na.rm = TRUE)) %>%
gather(var, value, M, SD) %>%
unite(label, label, var, sep = " ") %>%
spread(label, value) %>%
kable(format = "pandoc", digits = 2)| domain | wave | other M | other SD | self M | self SD | social M | social SD |
|---|---|---|---|---|---|---|---|
| academic | t1 | 0.00 | 0.92 | -0.13 | 0.95 | 0.06 | 0.91 |
| academic | t2 | 0.00 | 0.96 | -0.04 | 0.92 | 0.19 | 0.95 |
| academic | t3 | 0.03 | 0.89 | -0.04 | 0.82 | 0.21 | 0.88 |
| social | t1 | -0.02 | 0.94 | 0.00 | 0.91 | 0.22 | 0.91 |
| social | t2 | 0.00 | 0.96 | 0.00 | 0.95 | 0.30 | 0.98 |
| social | t3 | -0.01 | 0.96 | 0.05 | 0.89 | 0.33 | 0.90 |
neuro_model_data_dummy %>%
mutate(target = ifelse(target == .5, "self", "other"),
domain = ifelse(domain == .5, "social", "academic")) %>%
group_by(target, label, wave) %>%
summarize(M = mean(beta_std, na.rm = TRUE),
SD = sd(beta_std, na.rm = TRUE)) %>%
gather(var, value, M, SD) %>%
unite(label, label, var, sep = " ") %>%
spread(label, value) %>%
kable(format = "pandoc", digits = 2)| target | wave | other M | other SD | self M | self SD | social M | social SD |
|---|---|---|---|---|---|---|---|
| other | t1 | 0.00 | 0.92 | -0.10 | 0.92 | 0.16 | 0.90 |
| other | t2 | 0.00 | 0.97 | -0.14 | 0.94 | 0.27 | 0.98 |
| other | t3 | 0.02 | 0.92 | -0.10 | 0.85 | 0.27 | 0.88 |
| self | t1 | -0.02 | 0.94 | -0.03 | 0.94 | 0.11 | 0.92 |
| self | t2 | 0.00 | 0.94 | 0.11 | 0.92 | 0.22 | 0.95 |
| self | t3 | 0.01 | 0.93 | 0.11 | 0.86 | 0.27 | 0.90 |
visualize raw
hypothesis 0
domain_parc_plot_raw = neuro_model_data %>%
distinct(parcellation, target, domain, age, label, .keep_all = T) %>%
group_by(subjectID, wave, label, domain, parcellation) %>%
mutate(beta_std_avg = mean(beta_std, na.rm = TRUE)) %>%
ggplot(aes(x = age, y = beta_std_avg, color = domain)) +
geom_smooth(aes(group = interaction(parcellation, domain), size = label),
method = "lm", formula = y ~ poly(x, 2), se = FALSE, show.legend = FALSE) +
geom_smooth(aes(fill = domain), method = "lm", formula = y ~ poly(x, 2), size = 1.5) +
scale_color_manual(values = pal_social_academic) +
scale_fill_manual(values = pal_social_academic) +
scale_size_manual(values = c(.05, .1, .1)) +
scale_x_continuous(breaks = c(10, 13, 16)) +
scale_y_continuous(breaks = c(-1, 0, 1)) +
coord_cartesian(ylim = c(-1.2, 1.2)) +
facet_grid(~ label, labeller = parcel_labeller) +
labs(x = '\nage', y = 'mean standardized parameter estimate\n', color = '', fill = '') +
theme_minimal(base_size = 12) +
dcbw +
theme(legend.position = c(.85, .15),
legend.spacing.y = unit(.01, 'cm'),
legend.margin = unit(0, "cm"))
target_parc_plot_raw = neuro_model_data %>%
distinct(parcellation, target, domain, age, label, .keep_all = T) %>%
group_by(subjectID, wave, label, target, parcellation) %>%
mutate(beta_std_avg = mean(beta_std, na.rm = TRUE)) %>%
ggplot(aes(x = age, y = beta_std_avg, color = target)) +
geom_smooth(aes(group = interaction(parcellation, target), size = label),
method = "lm", formula = y ~ poly(x, 2), se = FALSE, show.legend = FALSE) +
geom_smooth(aes(fill = target), method = "lm", formula = y ~ poly(x, 2), size = 1.5) +
scale_color_manual(values = pal_self_other) +
scale_fill_manual(values = pal_self_other) +
scale_size_manual(values = c(.05, .1, .1)) +
scale_x_continuous(breaks = c(10, 13, 16)) +
scale_y_continuous(breaks = c(-1, 0, 1)) +
coord_cartesian(ylim = c(-1.2, 1.2)) +
facet_grid(~ label, labeller = parcel_labeller) +
labs(x = '\nage', y = 'mean standardized parameter estimate\n', color = '', fill = '') +
theme_minimal(base_size = 12) +
dcbw +
theme(legend.position = c(.85, .15),
legend.spacing.y = unit(.01, 'cm'),
legend.margin = unit(0, "cm"))
(h0_raw = cowplot::plot_grid(domain_parc_plot_raw, target_parc_plot_raw,
labels = c('A', 'B'), ncol = 2,
rel_widths = c(1, 1)))
hypothesis 1
domain_plot_raw = neuro_model_data %>%
distinct(parcellation, target, domain, age, label, .keep_all = T) %>%
group_by(subjectID, wave, label, domain, parcellation) %>%
mutate(beta_std_avg = mean(beta_std, na.rm = TRUE)) %>%
ggplot(aes(x = age, y = beta_std_avg, group = domain, color = domain)) +
geom_smooth(aes(fill = domain), method = 'lm', formula = y ~ poly(x,2), alpha = .2) +
scale_color_manual(values = pal_social_academic) +
scale_fill_manual(values = pal_social_academic) +
scale_x_continuous(breaks = c(10, 13, 16)) +
scale_y_continuous(breaks = round(seq(-.4, .6, .2), 1)) +
coord_cartesian(ylim = c(-.45, .65)) +
facet_grid(~ label, labeller = parcel_labeller) +
labs(x = '\nage', y = 'mean standardized parameter estimate\n', color = '', fill = '') +
dcbw +
theme(legend.position = "none")
soc_acad_plot_raw = neuro_model_data %>%
group_by(subjectID, age, label, domain, parcellation) %>%
mutate(beta_std_avg = mean(beta_std, na.rm = TRUE)) %>%
select(subjectID, age, label, domain, beta_std_avg) %>%
unique() %>%
spread(domain, beta_std_avg) %>%
mutate(avg_diff = social - academic) %>%
distinct(parcellation, age, label, .keep_all = T) %>%
ggplot(aes(x = age, y = avg_diff)) +
geom_smooth(aes(group = parcellation, size = label), method = "lm", formula = y ~ poly(x, 2),
se = FALSE, color = "grey50") +
geom_smooth(method = 'lm', formula = y ~ poly(x,2),
se = TRUE, color = pal_social_academic[2], fill = pal_social_academic[2], size = 1.5) +
scale_size_manual(values = c(.03, .1, .1)) +
scale_y_continuous(breaks = round(seq(-.4, .6, .2), 1)) +
coord_cartesian(ylim = c(-.45, .65)) +
scale_x_continuous(breaks = c(10, 13, 16)) +
facet_grid(~ label, labeller = parcel_labeller) +
labs(x = "\nage", y = "mean standardized BOLD signal value\n", color = '', fill = '') +
dcbw +
theme(legend.position = "none")
(h1_raw = cowplot::plot_grid(domain_plot_raw, soc_acad_plot_raw,
labels = c('A', 'B'), ncol = 2,
rel_widths = c(1, 1)))
hypothesis 2
target_plot_raw = neuro_model_data %>%
distinct(parcellation, target, domain, age, label, .keep_all = T) %>%
group_by(subjectID, wave, label, target, parcellation) %>%
mutate(beta_std_avg = mean(beta_std, na.rm = TRUE)) %>%
ggplot(aes(x = age, y = beta_std_avg, group = target, color = target)) +
geom_smooth(aes(fill = target), method = 'lm', formula = y ~ poly(x,2), alpha = .2) +
scale_color_manual(values = pal_self_other) +
scale_fill_manual(values = pal_self_other) +
scale_x_continuous(breaks = c(10, 13, 16)) +
scale_y_continuous(breaks = round(seq(-.4, .4, .2), 1)) +
coord_cartesian(ylim = c(-.4, .5)) +
facet_grid(~ label, labeller = parcel_labeller) +
labs(x = '\nage', y = 'mean standardized parameter estimate\n', color = '', fill = '') +
dcbw +
theme(legend.position = "none")
self_other_plot_raw = neuro_model_data %>%
group_by(subjectID, age, label, target, parcellation) %>%
mutate(beta_std_avf = mean(beta_std, na.rm = TRUE)) %>%
select(subjectID, age, label, target, beta_std_avf) %>%
unique() %>%
spread(target, beta_std_avf) %>%
mutate(avg_diff = self - other) %>%
distinct(parcellation, age, label, .keep_all = T) %>%
ggplot(aes(x = age, y = avg_diff)) +
geom_smooth(aes(group = parcellation, size = label), method = "lm", formula = y ~ poly(x, 2),
se = FALSE, color = "grey50") +
geom_smooth(method = 'lm', formula = y ~ poly(x,2),
se = TRUE, color = pal_self_other[2], fill = pal_self_other[2], size = 1.5) +
scale_size_manual(values = c(.03, .1, .1)) +
scale_y_continuous(breaks = round(seq(-.4, .4, .2), 1)) +
coord_cartesian(ylim = c(-.4, .5)) +
scale_x_continuous(breaks = c(10, 13, 16)) +
facet_grid(~ label, labeller = parcel_labeller) +
labs(x = "\nage", y = "mean standardized BOLD signal value\n", color = '', fill = '') +
dcbw +
theme(legend.position = "none")
(h2_raw = cowplot::plot_grid(target_plot_raw, self_other_plot_raw,
labels = c('A', 'B'), ncol = 2,
rel_widths = c(1, 1)))
hypothesis 3
int_plot_raw = neuro_model_data %>%
distinct(parcellation, target, domain, age, beta_std, label, .keep_all = T) %>%
ggplot(aes(x = age, y = beta_std, group = interaction(target, domain), color = domain, linetype = target)) +
geom_smooth(aes(fill = domain), method = 'lm', formula = y ~ poly(x,2), alpha = .2) +
scale_y_continuous(breaks = c(-.4, -.2, 0, .2, .4)) +
coord_cartesian(ylim = c(-.4, .45)) +
scale_color_manual(values = pal_social_academic) +
scale_fill_manual(values = pal_social_academic) +
scale_linetype_manual(name = "", values = c("dotted", "solid")) +
scale_x_continuous(breaks = c(10, 13, 16)) +
facet_grid(~ label, labeller = parcel_labeller) +
labs(x = '\nage', y = 'mean standardized parameter estimate\n', color = '', linetype = '', fill = '') +
guides(linetype = guide_legend(override.aes = list(color = "black"))) +
dcbw +
theme(legend.position = c(.75, .15),
legend.spacing.y = unit(.01, 'cm'),
legend.margin = unit(.5, "cm"),
legend.direction = "vertical",
legend.box = "horizontal")
soc_acad_int_plot_raw = neuro_model_data %>%
group_by(subjectID, age, label, target, domain, parcellation) %>%
mutate(beta_std_avg = mean(beta_std, na.rm = TRUE)) %>%
select(subjectID, age, label, target, domain, beta_std_avg) %>%
unique() %>%
spread(domain, beta_std_avg) %>%
mutate(avg_diff = social - academic) %>%
distinct(parcellation, age, label, .keep_all = T) %>%
ggplot(aes(x = age, y = avg_diff, color = target)) +
geom_smooth(aes(group = interaction(parcellation, target), size = label),
method = "lm", formula = y ~ poly(x, 2), se = FALSE, show.legend = FALSE) +
geom_smooth(aes(fill = target), method = 'lm', formula = y ~ poly(x,2),
se = TRUE, size = 1.5) +
scale_color_manual(values = pal_self_other) +
scale_fill_manual(values = pal_self_other) +
scale_size_manual(values = c(.03, .1, .1)) +
scale_y_continuous(breaks = round(seq(-.6, .6, .2), 1)) +
coord_cartesian(ylim = c(-.65, .65)) +
scale_x_continuous(breaks = c(10, 13, 16)) +
facet_grid(~ label, labeller = parcel_labeller) +
labs(x = "\nage", y = "mean standardized BOLD signal value\n", color = '', fill = '') +
dcbw +
theme(legend.position = c(.85, .15),
legend.spacing.y = unit(.01, 'cm'),
legend.margin = unit(0, "cm"))
self_other_int_plot_raw = neuro_model_data %>%
group_by(subjectID, age, label, domain, target, parcellation) %>%
mutate(beta_std_avg = mean(beta_std, na.rm = TRUE)) %>%
select(subjectID, age, label, domain, target, beta_std_avg) %>%
unique() %>%
spread(target, beta_std_avg) %>%
mutate(avg_diff = self - other) %>%
distinct(parcellation, age, label, .keep_all = T) %>%
ggplot(aes(x = age, y = avg_diff, color = domain)) +
geom_smooth(aes(group = interaction(parcellation, domain), size = label),
method = "lm", formula = y ~ poly(x, 2), se = FALSE, show.legend = FALSE) +
geom_smooth(aes(fill = domain), method = 'lm', formula = y ~ poly(x,2),
se = TRUE, size = 1.5) +
scale_color_manual(values = pal_social_academic) +
scale_fill_manual(values = pal_social_academic) +
scale_size_manual(values = c(.03, .1, .1)) +
scale_y_continuous(breaks = round(seq(-.6, .6, .2), 1)) +
coord_cartesian(ylim = c(-.65, .65)) +
scale_x_continuous(breaks = c(10, 13, 16)) +
facet_grid(~ label, labeller = parcel_labeller) +
labs(x = "\nage", y = "mean standardized BOLD signal value\n", color = '', fill = '') +
dcbw +
theme(legend.position = c(.85, .15),
legend.spacing.y = unit(.01, 'cm'),
legend.margin = unit(0, "cm"))
(h3_raw = cowplot::plot_grid(int_plot_raw, soc_acad_int_plot_raw, self_other_int_plot_raw,
labels = c('A', 'B', 'C'), ncol = 3))
run models
domain x age
model_domain_equation = formula(beta_std ~ 1 + age_c*domain*label +
age_c2*domain*label +
(1 + age_c*domain || subjectID) +
(1 + age_c*domain + age_c2*domain || parcellation))
model_domain_formula = lFormula(model_domain_equation, data = neuro_model_data_dummy)
model_domain_numFx = length(dimnames(model_domain_formula$X)[[2]])
model_domain_numRx = sum(as.numeric(lapply(model_domain_formula$reTrms$cnms, function(x) {
l <- length(x)
(l*(l - 1)) / 2 + l
})))
model_domain_maxfun = 10*(model_domain_numFx + model_domain_numRx + 1)^2
if (file.exists("../data/model_domain_dummy_2021.RDS")) {
model_domain = readRDS("../data/model_domain_dummy_2021.RDS")
} else {
model_domain = lmer(model_domain_equation, data = neuro_model_data_dummy, REML = F, #Use ML since we want to compare random effects
verbose = 2,
control = lmerControl(optCtrl = list(maxfun = model_domain_maxfun), optimizer = "bobyqa", calc.derivs = FALSE))
saveRDS(model_domain, "../data/model_domain_dummy_2021.RDS")
}
#summary(model_domain)domain x target x age
model_target_equation = formula(beta_std ~ 1 + age_c*target*domain*label +
age_c2*target*domain*label +
(1 + age_c*target*domain || subjectID) +
(1 + age_c*target*domain + age_c2*target*domain || parcellation))
model_target_formula = lFormula(model_target_equation, data = neuro_model_data_dummy)
model_target_numFx = length(dimnames(model_target_formula$X)[[2]])
model_target_numRx = sum(as.numeric(lapply(model_target_formula$reTrms$cnms, function(x) {
l <- length(x)
(l*(l - 1)) / 2 + l
})))
model_target_maxfun = 10*(model_target_numFx + model_target_numRx + 1)^2
if (file.exists("../data/model_target_dummy_2021.RDS")) {
model_target = readRDS("../data/model_target_dummy_2021.RDS")
} else {
model_target = lmer(model_target_equation, data = neuro_model_data_dummy, REML = F, #Use ML since we want to compare random effects
verbose = 2,
control = lmerControl(optCtrl = list(maxfun = model_target_maxfun), optimizer = "bobyqa", calc.derivs = FALSE))
saveRDS(model_target, "../data/model_target_dummy_2021.RDS")
}
#summary(model_target)compare models
anova(model_domain, model_target) %>%
as.data.frame() %>%
select(npar, AIC, Chisq, Df, `Pr(>Chisq)`) %>%
rownames_to_column() %>%
rename("model" = rowname,
"model df" = Df,
"X2" = Chisq,
"X2 df" = Df,
"p" = `Pr(>Chisq)`) %>%
mutate(AIC = round(AIC, 2),
X2 = round(X2, 2),
p = round(p, 3),
p = ifelse(p == 0, "< .001", gsub("0.(.*)", ".\\1", p))) %>%
mutate_if(is.numeric, funs(ifelse(is.na(.), "--", .))) %>%
mutate_if(is.character, funs(ifelse(is.na(.), "--", .))) %>%
kable(format = "pandoc")| model | npar | AIC | X2 | X2 df | p |
|---|---|---|---|---|---|
| model_domain | 29 | 462235.6 | – | – | – |
| model_target | 57 | 461963.7 | 327.95 | 28 | < .001 |
summarize best fitting model
model_target %>%
broom.mixed::tidy(effects = c("ran_pars", "fixed"), conf.int = TRUE) %>%
filter(effect == "fixed") %>%
select(-group) %>%
rename("b" = estimate,
"SE" = std.error,
"t" = statistic,
"p" = p.value) %>%
mutate(p = round(p, 3),
p = ifelse(p == 0, "< .001", gsub("0.(.*)", ".\\1", sprintf("%.3f", p))),
term = gsub("\\(Intercept\\)", "Intercept (age 13, label (control))", term),
term = gsub("target", "Target", term),
term = gsub("domain", "Domain", term),
term = gsub("labelself", "Label (self)", term),
term = gsub("labelsocial", "Label (social)", term),
term = gsub("age_c", "Age", term),
term = gsub(":", " x ", term),
term = gsub("sd__", "", term),
term = gsub("Observation", "observation", term),
effect = gsub("ran_pars", "random", effect),
`b [95% CI]` = ifelse(effect == "fixed", sprintf("%.3f [%.3f, %.3f]", b, conf.low, conf.high), "--")) %>%
mutate_if(is.numeric, round, 3) %>%
mutate_if(is.numeric, funs(ifelse(is.na(.), "--", .))) %>%
mutate_if(is.character, funs(ifelse(is.na(.), "--", .))) %>%
select(term, `b [95% CI]`, SE, t, df, p) %>%
kable(format = "pandoc")| term | b [95% CI] | SE | t | df | p |
|---|---|---|---|---|---|
| Intercept (age 13, label (control)) | -0.004 [-0.058, 0.049] | 0.027 | -0.157 | 389.202 | .875 |
| Age | 0.003 [-0.003, 0.008] | 0.003 | 0.975 | 165.622 | .331 |
| Target | 0.003 [-0.014, 0.021] | 0.009 | 0.364 | 179.471 | .716 |
| Domain | 0.009 [-0.016, 0.033] | 0.013 | 0.690 | 144.735 | .491 |
| Label (self) | -0.034 [-0.242, 0.175] | 0.107 | -0.315 | 356.532 | .753 |
| Label (social) | 0.242 [0.100, 0.385] | 0.073 | 3.328 | 356.480 | .001 |
| Age2 | 0.000 [-0.001, 0.001] | 0.001 | 0.280 | 599.799 | .780 |
| Age x Target | 0.002 [-0.003, 0.007] | 0.002 | 0.748 | 73.548 | .457 |
| Age x Domain | -0.002 [-0.009, 0.005] | 0.004 | -0.503 | 63.368 | .617 |
| Target x Domain | -0.009 [-0.044, 0.026] | 0.018 | -0.527 | 164.410 | .599 |
| Age x Label (self) | 0.007 [-0.008, 0.022] | 0.008 | 0.924 | 353.133 | .356 |
| Age x Label (social) | 0.018 [0.008, 0.029] | 0.005 | 3.511 | 352.651 | .001 |
| Target x Label (self) | 0.255 [0.198, 0.313] | 0.029 | 8.664 | 2045.761 | < .001 |
| Target x Label (social) | -0.051 [-0.090, -0.012] | 0.020 | -2.540 | 2030.155 | .011 |
| Domain x Label (self) | 0.066 [-0.003, 0.135] | 0.035 | 1.877 | 1009.675 | .061 |
| Domain x Label (social) | 0.118 [0.071, 0.165] | 0.024 | 4.908 | 1004.290 | < .001 |
| Target x Age2 | -0.002 [-0.004, -0.000] | 0.001 | -2.108 | 1427.460 | .035 |
| Domain x Age2 | -0.003 [-0.005, -0.001] | 0.001 | -3.046 | 1884.460 | .002 |
| Label (self) x Age2 | 0.001 [-0.003, 0.006] | 0.002 | 0.600 | 358.197 | .549 |
| Label (social) x Age2 | -0.004 [-0.007, -0.001] | 0.001 | -2.925 | 356.212 | .004 |
| Age x Target x Domain | 0.001 [-0.009, 0.012] | 0.005 | 0.263 | 69.501 | .794 |
| Age x Target x Label (self) | 0.026 [0.013, 0.039] | 0.007 | 3.911 | 186305.317 | < .001 |
| Age x Target x Label (social) | 0.006 [-0.003, 0.015] | 0.005 | 1.393 | 186299.729 | .164 |
| Age x Domain x Label (self) | -0.006 [-0.019, 0.007] | 0.007 | -0.914 | 186304.467 | .361 |
| Age x Domain x Label (social) | -0.005 [-0.013, 0.004] | 0.005 | -1.016 | 186297.730 | .310 |
| Target x Domain x Label (self) | -0.022 [-0.132, 0.088] | 0.056 | -0.393 | 186311.567 | .694 |
| Target x Domain x Label (social) | 0.097 [0.022, 0.172] | 0.038 | 2.547 | 186303.865 | .011 |
| Target x Domain x Age2 | 0.000 [-0.004, 0.004] | 0.002 | 0.057 | 1492.001 | .955 |
| Target x Label (self) x Age2 | -0.011 [-0.017, -0.004] | 0.003 | -3.164 | 186307.919 | .002 |
| Target x Label (social) x Age2 | 0.004 [-0.000, 0.009] | 0.002 | 1.852 | 186304.113 | .064 |
| Domain x Label (self) x Age2 | 0.006 [-0.000, 0.013] | 0.003 | 1.909 | 186314.601 | .056 |
| Domain x Label (social) x Age2 | 0.005 [0.001, 0.010] | 0.002 | 2.372 | 186302.120 | .018 |
| Age x Target x Domain x Label (self) | -0.006 [-0.032, 0.020] | 0.013 | -0.421 | 186304.080 | .673 |
| Age x Target x Domain x Label (social) | -0.014 [-0.031, 0.004] | 0.009 | -1.507 | 186298.997 | .132 |
| Target x Domain x Label (self) x Age2 | 0.009 [-0.005, 0.022] | 0.007 | 1.257 | 186307.980 | .209 |
| Target x Domain x Label (social) x Age2 | -0.001 [-0.010, 0.008] | 0.005 | -0.288 | 186301.661 | .773 |
# summarize random effects
print(VarCorr(model_target), comp = c("Variance","Std.Dev."), digits = 3)## Groups Name Variance Std.Dev.
## parcellation target:domain:age_c2 0.000000 0.00000
## parcellation.1 age_c:target:domain 0.000000 0.00000
## parcellation.2 domain:age_c2 0.000000 0.00000
## parcellation.3 target:age_c2 0.000000 0.00000
## parcellation.4 target:domain 0.000000 0.00000
## parcellation.5 age_c:domain 0.000000 0.00000
## parcellation.6 age_c:target 0.000000 0.00000
## parcellation.7 age_c2 0.000032 0.00566
## parcellation.8 domain 0.008080 0.08989
## parcellation.9 target 0.001437 0.03791
## parcellation.10 age_c 0.000859 0.02931
## parcellation.11 (Intercept) 0.198861 0.44594
## subjectID age_c:target:domain 0.000829 0.02878
## subjectID.1 target:domain 0.005907 0.07686
## subjectID.2 age_c:domain 0.000553 0.02351
## subjectID.3 age_c:target 0.000139 0.01181
## subjectID.4 domain 0.004338 0.06586
## subjectID.5 target 0.001406 0.03749
## subjectID.6 age_c 0.000158 0.01256
## subjectID.7 (Intercept) 0.002164 0.04651
## Residual 0.665033 0.81550simple slopes
run models
# self social > academic
self_social = emmeans::emtrends(model_target, pairwise ~ domain,
var = "age_c", at = list(target =.5, label="social"),
lmerTest.limit = 188577)$contrasts %>%
data.frame() %>%
mutate(contrast = "self social > academic",
parcel = "social",
age_effect = "linear") %>%
bind_rows(emmeans::emtrends(model_target, pairwise ~ domain,
var = "age_c2", at = list(target =.5, label="social"),
lmerTest.limit = 188577)$contrasts %>%
data.frame() %>%
mutate(contrast = "self social > academic",
parcel = "social",
age_effect = "quadratic"))
# social self > other
social_self = emmeans::emtrends(model_target, pairwise ~ target,
var = "age_c", at = list(domain =.5, label="self"),
lmerTest.limit = 188577)$contrasts %>%
data.frame() %>%
mutate(contrast = "social self > other",
parcel = "self",
age_effect = "linear") %>%
bind_rows(emmeans::emtrends(model_target, pairwise ~ target,
var = "age_c2", at = list(domain =.5, label="self"),
lmerTest.limit = 188577)$contrasts %>%
data.frame() %>%
mutate(contrast = "social self > other",
parcel = "self",
age_effect = "quadratic"))make table
social_self %>%
bind_rows(self_social) %>%
select(contrast, parcel, age_effect, estimate, SE, df, t.ratio, p.value) %>%
rename("b" = estimate,
"t" = t.ratio,
"p" = p.value) %>%
mutate(b = round(b, 3) * -1, #flip signs for it's .5 - (-.5)
SE = round(SE, 3),
df = round(df, 2),
t = abs(round(t, 2)),
p = round(p, 3)) %>%
kable(format = "pandoc")| contrast | parcel | age_effect | b | SE | df | t | p |
|---|---|---|---|---|---|---|---|
| social self > other | self | linear | 0.026 | 0.010 | 6704.64 | 2.70 | 0.007 |
| social self > other | self | quadratic | -0.008 | 0.005 | 133230.55 | 1.79 | 0.073 |
| self social > academic | social | linear | -0.013 | 0.007 | 684.47 | 1.76 | 0.079 |
| self social > academic | social | quadratic | 0.002 | 0.003 | 57999.28 | 0.53 | 0.595 |
visualize fitted models
reForm = as.formula("~(1 + age_c*target*domain + age_c2*target*domain || parcellation)")
neuro_plot_data = with(neuro_model_data_dummy,
expand.grid(target = unique(target),
domain = unique(domain),
parcellation = unique(parcellation),
age = unique(age),
stringsAsFactors = F)) %>%
mutate(label = ifelse(parcellation %in% self_parcels, 'self',
ifelse(parcellation %in% social_parcels, 'social', 'other')),
age_c = age - 13,
age_c2 = age_c^2,
subjectID = NA)
neuro_plot_data$expected = predict(model_target, newdata = neuro_plot_data, re.form = reForm)
neuro_plot_data$expected_mean = predict(model_target, newdata = neuro_plot_data, re.form = NA)
neuro_plot_data = neuro_plot_data %>%
mutate(target = factor(target, levels = c(-.5, .5), labels = c("other", "self")),
domain = factor(domain, levels = c(-.5, .5), labels = c("academic", "social")))hypothesis 0
domain_parc_plot = neuro_plot_data %>%
distinct(parcellation, target, domain, age, label, .keep_all = T) %>%
group_by(subjectID, age, label, domain, parcellation) %>%
mutate(expected_avg = mean(expected, na.rm = TRUE)) %>%
ggplot(aes(x = age, y = expected_avg, color = domain)) +
geom_smooth(aes(group = interaction(parcellation, domain), size = label), method = "lm", formula = y ~ poly(x, 2), se = FALSE, show.legend = FALSE) +
geom_smooth(method = "lm", formula = y ~ poly(x, 2), size = 1.25, se = FALSE) +
scale_color_manual(name = "", values = pal_social_academic) +
scale_size_manual(values = c(.05, .1, .1)) +
scale_x_continuous(breaks = c(10, 13, 16)) +
scale_y_continuous(breaks = c(-1, 0, 1)) +
coord_cartesian(ylim = c(-1.2, 1.2)) +
facet_grid(~label, labeller = parcel_labeller) +
labs(x = "\nage", y = "mean predicted BOLD signal value\n") +
dcbw +
theme(legend.position = c(.85, .15),
legend.spacing.y = unit(.01, 'cm'),
legend.margin = unit(0, "cm"))
target_parc_plot = neuro_plot_data %>%
distinct(parcellation, target, domain, age, label, .keep_all = T) %>%
group_by(subjectID, age, label, target, parcellation) %>%
mutate(expected_avg = mean(expected, na.rm = TRUE)) %>%
ggplot(aes(x = age, y = expected_avg, color = target)) +
geom_smooth(aes(group = interaction(parcellation, target), size = label), method = "lm", formula = y ~ poly(x, 2), se = FALSE, show.legend = FALSE) +
geom_smooth(method = "lm", formula = y ~ poly(x, 2), size = 1.25, se = FALSE) +
scale_color_manual(values = pal_self_other) +
scale_size_manual(values = c(.05, .1, .1)) +
scale_x_continuous(breaks = c(10, 13, 16)) +
scale_y_continuous(breaks = c(-1, 0, 1)) +
coord_cartesian(ylim = c(-1.2, 1.2)) +
facet_grid(~label, labeller = parcel_labeller) +
labs(x = "\nage", y = "mean predicted BOLD signal value\n", color = "") +
dcbw +
theme(legend.position = c(.85, .15),
legend.spacing.y = unit(.01, 'cm'),
legend.margin = unit(0, "cm"))
(h0_fitted = cowplot::plot_grid(domain_parc_plot, target_parc_plot,
labels = c('A', 'B'), ncol = 2,
rel_widths = c(1, 1)))
hypothesis 1
domain_plot = neuro_plot_data %>%
group_by(subjectID, age, label, domain, parcellation) %>%
mutate(expected_avg = mean(expected_mean, na.rm = TRUE)) %>%
distinct(parcellation, target, domain, age, label, .keep_all = T) %>%
ggplot(aes(x = age, y = expected_avg, color = domain)) +
geom_rect(data = subset(label_df, label == "social"), aes(fill = label, color = NA), alpha = .07,
xmin = -Inf, xmax = Inf, ymin = -Inf, ymax = Inf, show.legend = FALSE) +
geom_smooth(method = 'lm', formula = y ~ poly(x,2), alpha = .2, se = FALSE, size = 1.25) +
scale_y_continuous(breaks = seq(-.2, .45, .2)) +
coord_cartesian(ylim = c(-.25, .4)) +
scale_color_manual(values = pal_social_academic) +
scale_fill_manual(values = "lightgrey") +
scale_x_continuous(breaks = c(10, 13, 16)) +
facet_grid(~ label, labeller = parcel_labeller) +
labs(x = "\nage", y = "mean predicted BOLD signal value\n", color = '') +
dcbw +
theme(legend.position = c(.85, .15),
legend.spacing.y = unit(.01, 'cm'),
legend.margin = unit(0, "cm"))
soc_acad_plot = neuro_plot_data %>%
group_by(subjectID, age, label, domain, parcellation) %>%
mutate(expected_avg = mean(expected, na.rm = TRUE)) %>%
select(subjectID, age, label, domain, expected_avg) %>%
unique() %>%
spread(domain, expected_avg) %>%
mutate(expected_diff = social - academic) %>%
distinct(parcellation, age, label, .keep_all = T) %>%
ggplot(aes(x = age, y = expected_diff)) +
geom_rect(data = subset(label_df, label == "social"), aes(fill = label), alpha = .07,
xmin = -Inf, xmax = Inf, ymin = -Inf, ymax = Inf, show.legend = FALSE) +
geom_smooth(aes(group = parcellation, size = label), method = "lm", formula = y ~ poly(x, 2),
se = FALSE, color = "grey50") +
geom_smooth(method = 'lm', formula = y ~ poly(x,2),
se = FALSE, color = pal_social_academic[2], size = 1.5) +
scale_fill_manual(values = "lightgrey") +
scale_size_manual(values = c(.03, .1, .1)) +
scale_y_continuous(breaks = seq(-.2, .45, .2)) +
coord_cartesian(ylim = c(-.25, .4)) +
scale_x_continuous(breaks = c(10, 13, 16)) +
facet_grid(~ label, labeller = parcel_labeller) +
labs(x = "\nage", y = "mean predicted BOLD signal value\n", color = '') +
dcbw +
theme(legend.position = "none")
(h1_fitted = cowplot::plot_grid(domain_plot, soc_acad_plot,
labels = c('A', 'B'), ncol = 2,
rel_widths = c(1, 1)))
hypothesis 2
target_plot = neuro_plot_data %>%
group_by(subjectID, age, label, target, parcellation) %>%
mutate(expected_avg = mean(expected_mean, na.rm = TRUE)) %>%
distinct(parcellation, target, target, age, label, .keep_all = T) %>%
ggplot(aes(x = age, y = expected_avg, color = target)) +
geom_rect(data = subset(label_df, label == "self"), aes(fill = label, color = NA), alpha = .07,
xmin = -Inf, xmax = Inf, ymin = -Inf, ymax = Inf, show.legend = FALSE) +
geom_smooth(method = 'lm', formula = y ~ poly(x,2), alpha = .2, se = FALSE, size = 1.25) +
scale_y_continuous(breaks = seq(-.2, .3, .1)) +
coord_cartesian(ylim = c(-.2, .3)) +
scale_color_manual(values = pal_self_other) +
scale_fill_manual(values = "lightgrey") +
scale_x_continuous(breaks = c(10, 13, 16)) +
facet_grid(~ label, labeller = parcel_labeller) +
labs(x = "\nage", y = "mean predicted BOLD signal value\n", color = '') +
dcbw +
theme(legend.position = c(.85, .15),
legend.spacing.y = unit(.01, 'cm'),
legend.margin = unit(0, "cm"))
self_other_plot = neuro_plot_data %>%
group_by(subjectID, age, label, target, parcellation) %>%
mutate(expected_avg = mean(expected, na.rm = TRUE)) %>%
select(subjectID, age, label, target, expected_avg) %>%
unique() %>%
spread(target, expected_avg) %>%
mutate(expected_diff = self - other) %>%
distinct(parcellation, age, label, .keep_all = T) %>%
ggplot(aes(x = age, y = expected_diff)) +
geom_rect(data = subset(label_df, label == "self"), aes(fill = label), alpha = .07,
xmin = -Inf, xmax = Inf, ymin = -Inf, ymax = Inf, show.legend = FALSE) +
geom_smooth(aes(group = parcellation, size = label), method = "lm", formula = y ~ poly(x, 2),
se = FALSE, color = "grey50") +
geom_smooth(method = 'lm', formula = y ~ poly(x,2),
se = FALSE, color = pal_self_other[2], size = 1.5) +
scale_fill_manual(values = "lightgrey") +
scale_size_manual(values = c(.03, .1, .1)) +
scale_y_continuous(breaks = seq(-.2, .3, .1)) +
coord_cartesian(ylim = c(-.2, .3)) +
scale_x_continuous(breaks = c(10, 13, 16)) +
facet_grid(~ label, labeller = parcel_labeller) +
labs(x = "\nage", y = "mean predicted BOLD signal value\n", color = '') +
dcbw +
theme(legend.position = "none")
(h2_fitted = cowplot::plot_grid(target_plot, self_other_plot,
labels = c('A', 'B'), ncol = 2,
rel_widths = c(1, 1)))
hypothesis 3
int_plot = neuro_plot_data %>%
distinct(parcellation, target, domain, age, label, .keep_all = T) %>%
ggplot(aes(x = age, y = expected_mean, group = interaction(target, domain), color = domain, linetype = target)) +
geom_smooth(method = 'lm', formula = y ~ poly(x,2), alpha = 1, se = FALSE, size = 1.25) +
#geom_point() +
scale_y_continuous(breaks = c(-.4, .2, 0, .2, .4)) +
coord_cartesian(ylim = c(-.4, .45)) +
scale_color_manual(values = pal_social_academic) +
scale_linetype_manual(name = "", values = c("dotted", "solid")) +
scale_x_continuous(breaks = c(10, 13, 16)) +
facet_grid(~ label, labeller = parcel_labeller) +
labs(x = "\nage", y = "mean predicted BOLD signal value\n", color = '', linetype = '') +
guides(linetype = guide_legend(override.aes = list(color = "black"))) +
dcbw +
theme(legend.position = c(.75, .15),
legend.spacing.y = unit(.01, 'cm'),
legend.margin = unit(.5, "cm"),
legend.direction = "vertical",
legend.box = "horizontal")
soc_acad_int_plot = neuro_plot_data %>%
group_by(subjectID, age, label, target, domain, parcellation) %>%
mutate(expected_avg = mean(expected, na.rm = TRUE)) %>%
select(subjectID, age, label, target, domain, expected_avg) %>%
unique() %>%
spread(domain, expected_avg) %>%
mutate(expected_diff = social - academic) %>%
distinct(parcellation, age, label, .keep_all = T) %>%
ggplot(aes(x = age, y = expected_diff, color = target)) +
geom_smooth(aes(group = interaction(parcellation, target), size = label),
method = "lm", formula = y ~ poly(x, 2), se = FALSE, show.legend = FALSE) +
geom_smooth(method = 'lm', formula = y ~ poly(x,2),
se = FALSE, size = 1.5) +
scale_color_manual(values = pal_self_other) +
scale_size_manual(values = c(.03, .1, .1)) +
scale_y_continuous(breaks = c(-.4, .2, 0, .2, .4)) +
coord_cartesian(ylim = c(-.4, .45)) +
scale_x_continuous(breaks = c(10, 13, 16)) +
facet_grid(~ label, labeller = parcel_labeller) +
labs(x = "\nage", y = "mean predicted BOLD signal value\n", color = '') +
dcbw +
theme(legend.position = c(.85, .15),
legend.spacing.y = unit(.01, 'cm'),
legend.margin = unit(0, "cm"))
self_other_int_plot = neuro_plot_data %>%
group_by(subjectID, age, label, domain, target, parcellation) %>%
mutate(expected_avg = mean(expected, na.rm = TRUE)) %>%
select(subjectID, age, label, domain, target, expected_avg) %>%
unique() %>%
spread(target, expected_avg) %>%
mutate(expected_diff = self - other) %>%
distinct(parcellation, age, label, .keep_all = T) %>%
ggplot(aes(x = age, y = expected_diff, color = domain)) +
geom_smooth(aes(group = interaction(parcellation, domain), size = label),
method = "lm", formula = y ~ poly(x, 2), se = FALSE, show.legend = FALSE) +
geom_smooth(method = 'lm', formula = y ~ poly(x,2),
se = FALSE, size = 1.5) +
scale_color_manual(values = pal_social_academic) +
scale_size_manual(values = c(.03, .1, .1)) +
scale_y_continuous(breaks = c(-.4, .2, 0, .2, .4)) +
coord_cartesian(ylim = c(-.4, .45)) +
scale_x_continuous(breaks = c(10, 13, 16)) +
facet_grid(~ label, labeller = parcel_labeller) +
labs(x = "\nage", y = "mean predicted BOLD signal value\n", color = '') +
dcbw +
theme(legend.position = c(.85, .15),
legend.spacing.y = unit(.01, 'cm'),
legend.margin = unit(0, "cm"))
(h3_fitted = cowplot::plot_grid(int_plot, soc_acad_int_plot, self_other_int_plot,
labels = c('A', 'B', 'C'), ncol = 3))